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ftrCOOL (version 0.1.0)

Feature Extraction from Biological Sequences

Description

Extracts features from biological sequences. It contains most features which are presented in related work and also includes features which have never been introduced before. It extracts numerous features from Nucleotide and Peptide sequences. Each feature converts the input sequences to discrete numbers in order to use them as predictors in machine learning models. There are many features and information which are hidden inside a sequence. Utilizing the package, users can convert biological sequences to discrete models based on chosen properties. References: 'iLearn' 'Z. Chen et al.' (2019) . 'iFeature' 'Z. Chen et al.' (2018) . . 'PseKRAAC' 'Y. Zuo et al.' 'PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition' (2017) . 'iDNA6mA-PseKNC' 'P. Feng et al.' 'iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC' (2019) . 'I. Dubchak et al.' 'Prediction of protein folding class using global description of amino acid sequence' (1995) .

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Version

Install

install.packages('ftrCOOL')

Monthly Downloads

280

Version

0.1.0

License

GPL-3

Maintainer

Sare Amerifar

Last Published

August 31st, 2020

Functions in ftrCOOL (0.1.0)

APkNUCdi

Amphiphilic Pseudo-k Nucleotide Composition-di(series)
AutoCorTriNuc

Tri Nucleotide Autocorrelation-Autocovariance
APkNUCTri

Amphiphilic Pseudo-k Nucleotide Composition-Tri(series)
APAAC

Amphiphilic Pseudo-Amino Acid Composition(APAAC) (series)
AA2Binary

Amino Acid To Binary
AAKpartComposition

Amino Acid to K Part Composition
AutoCorDiNuc

Di Nucleotide Autocorrelation-Autocovariance
AAindex

Amino Acid Index
BLOSUM62

Blosum62
AAutoCor

Amino Acid Autocorrelation-Autocovariance
CTDD

CTDD(CTD Distribution)
CkSAApair

Composition of k-Spaced Amino Acids pairs
CTD

Composition_Transition_Distribution
CkSGAApair

Composition of k-Spaced Grouped Amino Acids pairs
CTDC

CTDC(CTD Composition)
Dinuc2Binary

Dinucleotide To Binary
CodonFraction

Codon Fraction
DiNucIndex

Di Nucleotide Index (DiNucIndex)
CkSNUCpair

Composition of k-Spaced Nucleotides Pairs
ExpectedValueAA

Expected Value for each Amino Acid
EffectiveNumberCodon

Effective Number of Codon
ExpectedValKmerNUC

Expected Value for k-mers(Nuc)
ExpectedValueGAA

Expected Value for Grouped Amino Acid
GrpDDE

Group Dipeptide Deviation from Expected Mean
LocalPoSpKnucF

Local Position Specific k Nucleotide Frequency
CTDT

CTDT(CTD Transition)
GCcontent

G_C content
GAAKpartComposition

Grouped Amino Acid K Part Composition
LocalPoSpKaaF

Local Position Specific k Amino Acids Frequency
ENUComposition

Enhanced nucleotide Composition
EIIP

Electron-ion interaction pseudopotentials (EIIP)
PseKRAAC_T14

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_14)
PseKRAAC_T15

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_15)
PSEkNCdi

Pseudo k Nucleotide Composition-Di(Parallel)
PSEkNCTri

Pseudo k Nucleotide Composition-Tri(Parallel)
CodonUsage

Codon Usage
ExpectedValueKmerAA

Expected Value for k-mers
PseKRAAC_T11

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_11)
EAAComposition

Enhanced Amino Acid Composition
DDE

Dipeptide Deviation from Expected Mean value
EGAAComposition

Enhanced Grouped Amino Acid Composition
PseKRAAC_T10

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_10)
ExpectedValueGKmerAA

Expected Value for Grouped k-mers
NUCKpartComposition

Nucleotide to K Part Composition
PseKRAAC_T3A

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_3B)
PseKRAAC_T16

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_16)
PseKRAAC_T6A

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_6A)
PseKRAAC_T6B

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_6B)
conjointTriadKS

k-Spaced Conjoint Triad
PseKRAAC_T3B

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_3B)
conjointTriad

Conjoint Triad
maxORFlength

Maximum Open Reading Frame length
PseKRAAC_T9

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_9)
nameKmer

nameKmer
kNUComposition

K Nucleotide Composition
QSOrder

Quasi Sequence Order
maxORF

Maximum Open Reading Frame
NUC2Binary

Nucleotide To Binary
revComp

reverseCompelement
novel_PseKNC

Novel Pseudo k Nucleotide Composition (series)
PseEIIP

Pseudo Electron-ion Interaction Pseudopotentials of Trinucleotide(PseEIIP)
PseKRAAC_T2

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_2)
fa.read

Fasta File Reader
alphabetCheck

AlphabetCheck
codonAdaptionIndex

Codon Adaption Index
PSEAAC

Pseudo-Amino Acid Composition(PSEAAC) (Parallel)
SAAC

Splitted Amino Acid Composition(SAAC)
PseKRAAC_T7

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_7)
PseKRAAC_T13

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_13)
PseKRAAC_T8

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_8)
PseKRAAC_T12

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_12)
fickettScore

Ficket Score
SGAAC

Splitted Group Amino Acid Composition(SGAAC)
needleman

Needleman-Wunsch
PseKRAAC_T1

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_1)
PseKRAAC_T5

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_5)
TriNucIndex

Tri Nucleotide Index (TriNucIndex)
kGAAComposition

K Grouped Amino Acid Composition
SOCNumber

Sequence Order Coupling Number
PseKRAAC_T4

Pseudo K_tuple Reduced Amino Acid Composition(PseKRAAComposition Type_4)
kAAComposition

K Amino Acid Composition
nonStandardSeq

nonStandard amino acid sequence
zSCALE

Z-SCALE